Merge pull request #221 from sigven/ensembl_v111

Update to Ensembl v111

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1.9000
+current_version = 1.4.1.9001
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?

.github/workflows/build_conda_recipes.yaml

@@ -5,12 +5,13 @@ on:
     branches:
       - master
       - bundle_update_2023
+      - ensembl_v111
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
   env_lock_path: conda/env/lock
-  VERSION: '1.4.1.9000' # versioned by bump2version
+  VERSION: '1.4.1.9001' # versioned by bump2version
 jobs:
   build_pcgrr_conda_pkg:
     # When merging to one of the branches above and the commit message matches

conda/env/yml/pcgr.yml

@@ -6,11 +6,11 @@ channels:
   - conda-forge
 
 dependencies:
-  - pcgr::pcgr ==1.4.1.9000 # versioned by bump2version
+  - pcgr::pcgr ==1.4.1.9001 # versioned by bump2version
   - bedtools
   - bcftools
   - cyvcf2
-  - ensembl-vep ==110.1
+  - ensembl-vep ==111.0
   - htslib
   - pandoc
   - bioconda::perl-bio-bigfile

conda/env/yml/pcgrr.yml

@@ -7,7 +7,7 @@ channels:
 
 dependencies:
   - python
-  - pcgr::r-pcgrr ==1.4.1.9000 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9001 # versioned by bump2version
   - pcgr::r-cpsr
   - r-argparse
   - bioconductor-bsgenome.hsapiens.ucsc.hg38

conda/env/yml/pkgdown.yml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - pcgr::r-pcgrr ==1.4.1.9000 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9001 # versioned by bump2version
   - r-pkgdown
   - r-readr
   - pandoc

conda/recipe/pcgrr/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: r-pcgrr
-  version: 1.4.1.9000 # versioned by bump2version
+  version: 1.4.1.9001 # versioned by bump2version
 
 source:
   path: ../../../pcgrr

pcgr/_version.py

@@ -1,2 +1,2 @@
 # versioned by bump2version
-__version__ = '1.4.1.9000'
+__version__ = '1.4.1.9001'

pcgrr/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pcgrr
 Type: Package
 Title: Personal Cancer Genome ReporteR
-Version: 1.4.1.9000
+Version: 1.4.1.9001
 Date: 2023-12-30
 Authors@R:
     c(person(given = "Sigve",

pcgrr/vignettes/installation.Rmd

@@ -12,7 +12,7 @@ output: rmarkdown::html_document
   software requirements:
 
 ```bash
-PCGR_VERSION="1.4.1.9000"
+PCGR_VERSION="1.4.1.9001"
 PCGR_REPO="https://raw.githubusercontent.com/sigven/pcgr/v${PCGR_VERSION}/conda/env/lock/"
 PLATFORM="linux" # or "osx"
 
@@ -79,7 +79,7 @@ Download and unpack the latest software release from <https://github.com/sigven/
 Alternatively if you have `git` installed, you can do:
 
 ```bash
-PCGR_VERSION="1.4.1.9000"
+PCGR_VERSION="1.4.1.9001"
 OUTPUT_DIRECTORY="PCGR"
 
 git clone \
@@ -235,7 +235,7 @@ docker container run -it --rm \
     -v /Users/you/dir1/data:/root/pcgr_data \
     -v /Users/you/dir2/pcgr_inputs:/root/pcgr_inputs \
     -v /Users/you/dir3/pcgr_outputs:/root/pcgr_outputs \
-    sigven/pcgr:1.4.1.9000 \
+    sigven/pcgr:1.4.1.9001 \
     pcgr \
       --input_vcf "/root/pcgr_inputs/tumor_sample.BRCA.vcf.gz" \
       --pcgr_dir "/root/pcgr_data" \

setup.py

@@ -2,7 +2,7 @@
 
 setuptools.setup(
     name='pcgr',
-    version='1.4.1.9000', # versioned by bump2version
+    version='1.4.1.9001', # versioned by bump2version
     license='MIT',
     author='Sigve Nakken',
     author_email='sigven@gmail.com',